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Principles for computational design of antibodies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QQ9 3QQ9, 4JFZ experimental model PDB 4JFZ 3QQ9, 4JFZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M NH4CH3CO2
0.05M Mg(CH3CO2)2
0.05M Cacodylate pH=6.5
15% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.48 50.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.909 α = 90 b = 67.909 β = 90 c = 182.181 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2014-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 60.73 93 0.074 6.5 10.9 28196
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 85.9 0.59 1.3 10.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3QQ9, 4JFZ 2.1 60.73 27279 1405 97.84 0.2199 0.21794 0.2578 0.2721 RANDOM 54.799
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.46 0.23 0.46 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.132 r_dihedral_angle_4_deg 21.315 r_dihedral_angle_3_deg 13.997 r_dihedral_angle_1_deg 7.239 r_long_range_B_refined 6.405 r_long_range_B_other 6.404 r_scangle_other 4.571 r_mcangle_it 3.842 r_mcangle_other 3.841 r_scbond_it 2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.132 r_dihedral_angle_4_deg 21.315 r_dihedral_angle_3_deg 13.997 r_dihedral_angle_1_deg 7.239 r_long_range_B_refined 6.405 r_long_range_B_other 6.404 r_scangle_other 4.571 r_mcangle_it 3.842 r_mcangle_other 3.841 r_scbond_it 2.97 r_scbond_other 2.969 r_mcbond_it 2.603 r_mcbond_other 2.6 r_angle_refined_deg 1.45 r_angle_other_deg 0.909 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3303 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALEPACK data scaling PHASER phasing